Opened up the Remote Access management console and You see red. The red color is nice but in this case it means that something is wrong.

We needed to reset WAP configuration, in Registry we changed value 2 = configured to the Value 1 = not configured

Use powershell.exe – Install-WebApplicationProxy -CertificateThumbprint “xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx” -FederationServiceName “xxxxxx.com” (but it did not work for me same good as GUI for server ADFS 3.0 S2K12 R2 🙁 ….)

or through console Remote Access management we configured WAP again. It requires name of ADFS service – xxxxxxxxxxx.com, usually service account – axxxxxx and choose the right certificate – right ADFS certificate with name xxxxxxxxxxx.com. Although we did this, the service tried to use different, self-signed certificate , In ADFS event log we could see „Unable to retrieve proxy configuration data from the Federation Service + thumbprint of bad certificate not our ADFS certificate “ In mmc.exe we could see only the certificate for MS SCOM, xxxxxxxxxxx.com and some expirated self-signed certificates but we could not see the certificate with thumbprint found in event log. By Powershell we could list it (example is below), we found bad certificate + others and we removed all certificates self-signed certificate.

When we removed the self-signed certificates, we tried to complete the wizard again and it was success

Now it is working well. Do not worry that we see server xxxxxx twice, we could see it because in my case we configured WAP after the server has been configured with postfix (full computer name), because for MS SCOM monitoring it is require.

/B Abort if an error is encountered. By default, CIPHER continues
executing even if errors are encountered.
/C Displays information on the encrypted file.
/D Decrypts the specified files or directories.
/E Encrypts the specified files or directories. Directories will be
marked so that files added afterward will be encrypted. The
encrypted file could become decrypted when it is modified if the
parent directory is not encrypted. It is recommended that you
encrypt the file and the parent directory.
/H Displays files with the hidden or system attributes. These files
are omitted by default.
/K Creates a new certificate and key for use with EFS. If this
option is chosen, all the other options will be ignored.

Note: By default, /K creates a certificate and key that conform
to current group policy. If ECC is specified, a self-signed
certificate will be created with the supplied key size.

/N This option only works with /U. This will prevent keys being
updated. This is used to find all the encrypted files on the
local drives.
/R Generates an EFS recovery key and certificate, then writes them
to a .PFX file (containing certificate and private key) and a
.CER file (containing only the certificate). An administrator may
add the contents of the .CER to the EFS recovery policy to create
the recovery key for users, and import the .PFX to recover
individual files. If SMARTCARD is specified, then writes the
recovery key and certificate to a smart card. A .CER file is
generated (containing only the certificate). No .PFX file is
generated.

Note: By default, /R creates an 2048-bit RSA recovery key and
certificate. If ECC is specified, it must be followed by a
key size of 256, 384, or 521.

/S Performs the specified operation on the given directory and all
files and subdirectories within it.
/U Tries to touch all the encrypted files on local drives. This will
update user’s file encryption key or recovery keys to the current
ones if they are changed. This option does not work with other
options except /N.
/W Removes data from available unused disk space on the entire
volume. If this option is chosen, all other options are ignored.
The directory specified can be anywhere in a local volume. If it
is a mount point or points to a directory in another volume, the
data on that volume will be removed.
/X Backup EFS certificate and keys into file filename. If efsfile is
provided, the current user’s certificate(s) used to encrypt the
file will be backed up. Otherwise, the user’s current EFS
certificate and keys will be backed up.
/Y Displays your current EFS certificate thumbnail on the local PC.
/ADDUSER Adds a user to the specified encrypted file(s). If CERTHASH is
provided, cipher will search for a certificate with this SHA1
hash. If CERTFILE is provided, cipher will extract the
certificate from the file. If USER is provided, cipher will
try to locate the user’s certificate in Active Directory Domain
Services.
/FLUSHCACHE
Clears the calling user’s EFS key cache on the specified server.
If servername is not provided, cipher clears the user’s key cache
on the local machine.
/REKEY Updates the specified encrypted file(s) to use the configured
EFS current key.
/REMOVEUSER
Removes a user from the specified file(s). CERTHASH must be the
SHA1 hash of the certificate to remove.

Used without parameters, CIPHER displays the encryption state of the
current directory and any files it contains. You may use multiple directory
names and wildcards. You must put spaces between multiple parameters.